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- PDB-3kd5: Closed ternary complex of an RB69 gp43 fingers domain mutant comp... -

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Basic information

Entry
Database: PDB / ID: 3kd5
TitleClosed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.
Components
  • DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / polymerase / gp43 / human cytomegalovirus / hcmv / acyclic guanosine / acyclovir / phosphonoformic acid / foscarnet / foscavir / antiviral / DNA replication / DNA-binding / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, palm domain / Palm domain of DNA polymerase / B family DNA polymerase, finger domain / DNA polymerase, palm domain superfamily ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, palm domain / Palm domain of DNA polymerase / B family DNA polymerase, finger domain / DNA polymerase, palm domain superfamily / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / Monooxygenase / DNA polymerase family B, exonuclease domain / DNA polymerase family B / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHONOFORMIC ACID / DNA (> 10) / DNA / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 2.69 Å
AuthorsZahn, K.E. / Doublie, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase.
Authors: Zahn, K.E. / Tchesnokov, E.P. / Gotte, M. / Doublie, S.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
P: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3')
E: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7777
Polymers115,5783
Non-polymers1994
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-57 kcal/mol
Surface area44460 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)77.855, 122.481, 133.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules TP

#1: DNA chain DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')


Mass: 5492.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide was chemically synthesized.
#2: DNA chain DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3')


Mass: 4278.780 Da / Num. of mol.: 1 / Fragment: Acyclic GMP terminated primer DNA / Source method: obtained synthetically / Details: Oligonucleotide was chemically synthesized.

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Protein , 1 types, 1 molecules E

#3: Protein DNA polymerase / / Gp43


Mass: 105806.359 Da / Num. of mol.: 1
Fragment: RB69 gp43 exo- chimera containing elements from the fingers domain of the human cytomegalovirus DNA polymerase.
Mutation: D222A V478W F479V N480S I557M N558A R559L L561V I562T I563C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (bacteriophage)
Gene: 43, RB69 gp43 / Plasmid: pPR-IBA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q38087, DNA-directed DNA polymerase

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Non-polymers , 3 types, 250 molecules

#4: Chemical ChemComp-PPF / PHOSPHONOFORMIC ACID / Foscarnet


Mass: 126.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3O5P / Comment: medication, antivirus, inhibitor*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% PEG 20000, 0.1M sodium acetate pH5, 0.1M magnesium acetate, 0.1M Tris HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03315 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2009
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet ry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 36065 / Num. obs: 36065 / % possible obs: 100 % / Redundancy: 23.4 % / Biso Wilson estimate: 86.5 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 26.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 21.1 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3545 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0041refinement
CNSrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: isomorphous replacement
Starting model: PDB entry 3KD1
Resolution: 2.69→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 25.02 / SU ML: 0.32 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26317 3470 9.6 %Test set extracted from 1IG9
Rwork0.21467 ---
all0.21939 32507 --
obs0.21939 32507 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.787 Å2
Baniso -1Baniso -2Baniso -3
1--5.64 Å20 Å20 Å2
2--0.5 Å20 Å2
3---5.14 Å2
Refinement stepCycle: LAST / Resolution: 2.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7379 648 10 246 8283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0218292
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.911342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7325904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67124.182373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.703151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7321545
X-RAY DIFFRACTIONr_chiral_restr0.0670.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216125
X-RAY DIFFRACTIONr_mcbond_it0.0230.247665
LS refinement shellResolution: 2.686→2.755 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 235 -
Rwork0.347 2097 -
obs-2332 89.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5858-0.2008-0.29899.1178-2.81292.65470.1878-0.2390.29070.2886-0.111-1.4607-0.06260.2946-0.07680.1992-0.0449-0.18680.2718-0.01350.910128.10562.62835.568
23.52933.3954-1.51394.3271-1.26812.96730.020.0259-0.3613-0.0222-0.0029-1.2350.01320.1171-0.01710.18170.0807-0.11980.22120.0110.913519.15855.56329.498
32.69730.65620.3793.1633-0.14481.98450.141-0.32640.0240.9255-0.0982-0.46380.2417-0.1871-0.04280.7721-0.0049-0.43810.3417-0.02650.35568.82537.06451.871
43.36491.2906-0.60373.23540.19581.739-0.05640.8380.8149-0.50070.2369-0.4721-0.376-0.2933-0.18050.33210.08480.16850.47980.3310.49881.47461.4299.632
52.27040.3105-0.02372.23240.77091.4025-0.02850.96010.0547-0.43420.0651-0.3221-0.0222-0.2775-0.03660.29860.06480.1060.68140.11980.1769-4.60445.1735.549
62.4606-1.1485-0.07439.42142.42271.1425-0.13110.2342-0.50410.67890.1735-0.6030.32130.2639-0.04240.32250.11150.00390.32320.08630.51359.41831.35518.748
74.53371.3810.58753.56640.82752.45860.2577-0.3178-0.20840.9773-0.25920.0870.2979-0.63490.00150.5418-0.07190.04260.48380.0640.0293-22.91138.4535.958
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 108
2X-RAY DIFFRACTION2E340 - 382
3X-RAY DIFFRACTION3E109 - 339
4X-RAY DIFFRACTION4E383 - 468
5X-RAY DIFFRACTION5E573 - 729
6X-RAY DIFFRACTION6E469 - 572
7X-RAY DIFFRACTION7E730 - 905

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